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Registration Open for ELIXIR-NL Course Bioinformatics for Translational Medicine using Galaxy: see it, do it, teach it! - 17- 19 October 2018, Amsterdam
by Celia van Gelder 13 Jul '18

13 Jul '18

*ELIXIR-NL Course: * Bioinformatics for Translational Medicine using Galaxy: see it, do it, teach it! Please circulate this email to those who might be interested. Date: 17-19 October, 2018 Location: VU Amsterdam (O|2 Lab Building <https://goo.gl/maps/CphwJEFDegt>, Gustav Mahlerlaan 665, 1082 MK, 1082 MK Amsterdam) Organizers: This course is an ELIXIR-EXCELERATE course and is organised by ELIXIR-NL by Chao (Cico) Zhang (VU), Sanne Abeln (VU), Anton Feenstra (VU), Saskia Hiltemann (ErasmusMC), Mateusz Kuzak (DTL) and Celia van Gelder (DTL). Course page (incl. Application Form): https://www.biosb.nl/education/course-portfolio/bioinformatics-for-translat… TARGET AUDIENCE 1) Biomedical & translational medicine researchers/students who are keen on bioinformatics and 2) educators in the “bio” domain who would like to start using Galaxy in their courses as an introduction to Bioinformatics. COURSE DESCRIPTION Analysing molecular data in translational medicine involves a multitude of computational steps. Here, we introduce the basics of how to design and run these steps within Galaxy, a free and easy-to-use web platform that enables users to connect bioinformatics tools into a workflow without any prior programming expertise. This course consists of two parts. Part 1 will let you get familiar with Galaxy; it will introduce some bioinformatics workflows used for RNAseq, variant detection and metagenomics; and how to easily connect different computational steps in Galaxy. Part 2 will focus on how to teach bioinformatics with Galaxy and to design bioinformatics courses using Galaxy. Participants can register for both parts separately. This course is also interspersed with a few keynotes, from recognised researchers in the fields of Biomedicine, Bioinformatics education and Galaxy workflows. The confirmed speakers include Jaap Heringa, who is the scientific director of the Netherlands Bioinformatics Centre; and Björn Grüning, who is the leader of Galaxy training network, also actively involved in Bioconda. PREREQUISITE KNOWLEDGE The attendees of Part I are assumed to have the basic knowledge of biomedicine (molecular biology and genomics) and be interested in analysing patient derived sequencing data. The attendees of Part II are assumed to have some teaching experience in the relevant field (e.g., bioinformatics, computational biology, systems biology, quantitative biology, etc.) COURSE SCHEDULE The course consists of six modules, as the table below shows, covering a list of topics as follows: - Introduction to Galaxy. Run bioinformatics tools and workflows in Galaxy without the need for any programming expertise. - Reference-based RNA-Seq data analysis - Module detection in differential gene expression in meta transcriptomics samples. - Microbiota Analysis: 16S rRNA sequencing analysis in Galaxy - How to teach bioinformatics workflows. - Galaxy setup for teaching and training material development. Day 1 - Wed Oct 17 Day 2 - Thur Oct 18 Day 3 - Frid Oct 19 Morning Galaxy 101 + Variant detection <http://galaxyproject.github.io/training-material/topics/introduction/> Network analysis with microbiota metatranscriptome <https://www.ncbi.nlm.nih.gov/pubmed/26342232> Teaching bioinformatics workflows Saskia Hiltemann <https://shiltemann.github.io/> Chao Zhang <https://hi-it.org/> Anton Feenstra <http://www.few.vu.nl/~feenstra/> Keynote Speech* I: About bioinformatics workflows II: About Galaxy and ELIXIR III: About bioinformatics teaching TBD Björn Grüning <https://galaxyproject.org/people/bjoern-gruening/> Jaap Heringa <https://www.cs.vu.nl/~heringa/> Afternoon BWA + RNAseq <http://galaxyproject.github.io/training-material/topics/transcriptomics/> 16S rRNA sequencing with mothur <http://galaxyproject.github.io/training-material/topics/metagenomics/> Galaxy training material development <http://galaxyproject.github.io/training-material/> Saskia Hiltemann <https://shiltemann.github.io/> Saskia Hiltemann <https://shiltemann.github.io/> Saskia Hiltemann <https://shiltemann.github.io/> Evening Social dinner About the instructors: Each session is led by one instructor listed in the table above but strongly supported by multiple co-instructors, including, but not limited to, Saskia Hiltemann (ErasmusMC), Chao Zhang (VU), Leon Mei (LUMC), Ruben Vorderman (LUMC) and Sanne Abeln (VU). Note: The course is held in a computer classroom, so you don’t need to bring your own laptop. COURSE FEE Course participation is free of charge. A workshop dinner will be organized on Thursday (at participants’ own expenses) Should you have any question about this course, please contact Celia van Gelder (celia.van.gelder(a)dtls.nl) Dr. Celia W.G. van Gelder Programme Manager DTL Learning Training Coordinator ELIXIR-NL ELIXIR Training Platform Leader tel. +31613375327 e-mail: celia.van.gelder(a)dtls.nl websites: www.dtls.nl, www.biosb.nl skype: celia.van.gelder Office: DTL | Jaarbeurs Innovation Mile (JIM) | 6th floor Beatrixgebouw | Jaarbeursplein 6 | 3521 AL Utrecht Postal address: Postbus 8500 | 3503 RM Utrecht While I may be sending this email outside my normal office hours, I have no expectation to receive a reply outside yours.

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Available (permanent) positions in Sweden
by Lieven Sterck 13 Jul '18

13 Jul '18

> From: "Henrik Lantz" <henrik.lantz(a)nbis.se> > To: "Lieven Sterck" <lieven.sterck(a)psb.vib-ugent.be> > Sent: Wednesday, 11 July, 2018 11:48:20 > Subject: Available positions in Sweden > Hi Lieven, > We have two new permanent positions available in Lund in the Southernmost part > of Sweden. The positions focus on support to Swedish researchers under a > fee-for-service model and will most likely involve working with RNA-seq data. > As the positions are permanent I was thinking that there might be an interest > also in other countries, and I would appreciate if you could spread the below > link to interested people in Belgium. > https://lu.mynetworkglobal.com/en/what:job/jobID:216986/ > Cheers, > Henrik

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Bioinformatician position: computational cancer biology
by Lodewyk Wessels 12 Jul '18

12 Jul '18

BIOINFORMATICIAN POSITION EARLY DETECTION OF OVARIAN CANCER and INTEGRATION OF TISSUE SPATIAL MAPS AND GENE EXPRESSION The research groups of Lodewyk Wessels, Frederic Amant and Christianne Lok are looking for a motivated and talented Computational Biologist to join their teams at the Netherlands Cancer Institute (NKI). PROJECT DESCRIPTIONS. Early detection of Ovarian cancer. Differentiation between benign growth and ovarian tumors before surgery is currently far from optimal. This leads to a significant fraction of ovarian tumors going undetected and also a large fraction of benign growths being unnecessarily treated in specialized settings. In this project we will be employing innovative non-invasive sampling of peripheral blood to develop a more accurate test for the detection of ovarian tumors. We will employ two strategies. First we will isolate and perform RNAseq profiling on tumor educated platelets (TEP). Second, we will perform DNA sequencing and to detect abnormal DNA copy number profiles from the circulating tumor DNA (ctDNA). For both datasets, the successful candidate will build classifiers to accurately distinguish ovarian cancer from benign growths. Integration of gene expression and tissue imaging to study post-partum breast cancer. Breast cancers that occur 1 to 2 years after childbirth (postpartum breast cancer) have a particularly poor outcome. It has been hypothesized that (immunological) changes in the breast, occurring after childbirth, are underlying the poor prognosis of postpartum breast cancer. In this project we will investigate postpartum breast cancer by combining two unique data sets across 400 patients. Tumors will be subjected to RNA-sequencing as well as spatial tissue profiling for a panel of immune markers employing the VECTRA technology. The spatial profiling provides the location of cells in a cross section of the tumor as well as the expression of the recorded markers in each cell. This allows a detailed characterization of the tumor and the surrounding stroma, indicating which cells occur in the stroma, their position with respect to each other and with respect to the tumor cells. The successful candidate will perform computational analysis of these datasets separately and in an integrated fashion to study the mechanisms that underlie postpartum breast cancer. CANDIDATE PROFILE. We are seeking a highly motivated bioinformatician with: • A degree in bioinformatics, computer science or a related discipline • Experience with high-throughput data analysis, especially sequencing data • Proficiency in bioinformatics programming languages (e.g. R, Python) • Good cross-disciplinary collaborative and communication skills • Experience in statistics, machine learning and/or image processing is a plus • Experience in cancer biology and clinical applications is a plus INTERESTED? Please send CV and motivation letter to Lodewyk Wessels (l.wessels(a)nki.nl) and Patty Lagerweij (p.lagerweij(a)nki.nl) Please include the names and contact information of at least two references. For further information on the Wessels group (Computational Cancer Biology) please visit our home page https://ccb.nki.nl/

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Discrete models and formal verification in biology - 29-31 August 2018 - open for registration!
by Anton Feenstra 12 Jul '18

12 Jul '18

Dear colleagues, You may be interested in a workshop on "Discrete models and formal verification in biology" that will be hosted by Ben Hall, from 29-31 August 2018, Murray Edwards College Cambridge For more information and registration, please refer to https://discretebiology.com/ Best, Anton. -- Groetjes, Anton _____________ _______________________________________________________ | | | | _ _ ___,| K. Anton Feenstra | | / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam | |( | )| | | De Boelelaan 1081 - 1081 HV Amsterdam - Netherlands | | \_/ \_/ | | | Tel: +31 20 59 87783 - skype: kafeenstra - room S404 | | | Feenstra(a)few.vu.nl - www.few.vu.nl/~feenstra/ | | | "Studying expands knowledge. Knowledge is power. | | | Power corrupts. Corruption is a crime. Crime doesn't | | | pay." (Anonymous) | |_____________|_______________________________________________________|

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October training workshops at Edinburgh Genomics: Linux for Genomics, Intro to RNAseq Analysis and Intro to Python
by DUNBAR Donald 10 Jul '18

10 Jul '18

Hello all, we have some new dates in October for our popular Edinburgh Genomics training workshops<https://genomics.ed.ac.uk/services/training>. We now offer registration, on a first come first served basis, to our Linux for Genomics, Introduction to RNAseq Data Analysis, and Introduction to Python for Biologists workshops developed and taught by our Edinburgh Genomics Bioinformaticians and our training partner Dr Martin Jones. 1. Linux for Genomics, Monday 1st October 2018 REGISTER NOW<https://www.surveymonkey.co.uk/r/L4G_011018> 2. Introduction to RNAseq Data Analysis, Tuesday 2nd to Wednesday 3rd October 2018 REGISTER NOW<https://www.surveymonkey.co.uk/r/I2R_021018><https://www.surveymonkey.co.uk/r/6QQVF7D> 3. Introduction to RNAseq Data Analysis, Thursday 4th to Friday 5th October 2018 REGISTER NOW<https://www.surveymonkey.co.uk/r/I2R_041018> 4. Introduction to Python for Biologists, Monday 22nd to Friday 26th October 2018 REGISTER NOW<https://www.surveymonkey.co.uk/r/ZBVFTQ3> Please use the links provided above to register for a place. These workshops are very popular and have limited places, so please do register as early as you can. After registration, you will be asked for payment and then your place will be confirmed. Cancellation up to one month before the workshop will allow a refund minus an admin fee. See course details on our training pages: * https://genomics.ed.ac.uk/services/training * https://genomics.ed.ac.uk/services/introduction-rna-seq-data-analysis * https://genomics.ed.ac.uk/services/linux-genomics * https://genomics.ed.ac.uk/services/introduction-python-biologists-0 Please let me know if you have any questions or comments. Feel free to share with colleagues and contacts. We plan to offer an 'R for Genomics' and an 'Advanced Linux: Cloud, Cluster and Pipeline Programming' early in 2019, and we will let you know when these are available. With best wishes and we look forward to welcoming you to Edinburgh Genomics. Donald --- Dr Donald Dunbar Bioinformatics Operations Manager Edinburgh Genomics, Genome Science Ashworth Labs, The King's Buildings The University of Edinburgh donald.dunbar(a)ed.ac.uk Edinburgh Genomics' Privacy Notice can be viewed at: http://genomics.ed.ac.uk/about-us/privacy-notice This email and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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PPB18 - Hands-on Training Course on Programming in Python - Announcement / Reminder
by Pedro L. Fernandes 10 Jul '18

10 Jul '18

Course Announcement / Reminder PPB18 Programming in Python (for Biologists, but not only) with Allegra Via, Vincenza Colonna and David P. Judge Key terms: Programming, Python IMPORTANT DATES for this Course Deadline for applications: July 18th 2018 Latest notification of acceptance: July 19th 2018 Course date: July 23rd - July 27th 2018 The GTPB is proud to announce that the above referenced hands-on training course is open for applications Admission: Candidates with adequate profile will be accepted in the next 72 hours after the application until we reach 20 participants. Course description: Python is a programming language that is ideal for data processing. The course will start from zero knowledge, and will introduce the participants to all the basic concepts of programming such as calculating, repeating things, making choices, reading and writing files, filtering and organising data, program logic and writing larger programs. The examples and practical sessions will mostly focus on managing biological data. In particular the sessions will cover: - parsing common file formats (Uniprot, GenBank, PDB, BLAST) - data retrieval from files and their manipulation - finding motifs in sequences - manipulating tables - plotting data The course will be highly interactive and the participants will continuously put theory into practice while learning. At the end of the course, the participants will have a good understanding of programming basics and will have acquired the skills to manage bioinformatics database record and data files. Basic Unix/Linux skills will be provided at the beginning of the course. Participants are welcome to bring to the course the "typical" text file that they may need to filter, manipulate or analyse such a table, a file in fastq or fasta format, a PDB file, etc. The course is directed to biologists with little or no programming experience and aims at making them capable to use Python to autonomously manage and analyse biological data. More information at the GTPB website, http://gtpb.igc.gulbenkian.pt/bicourses/2018/PPB18// Hoping that this course meets your interests, Pedro Fernandes -- The Gulbenkian Training Programme in Bioinformatics Pedro L. Fernandes, Organiser Instituto Gulbenkian de Ciência Rua da Quinta Grande, 6 2780-156 OEIRAS Portugal -- Pedro L. Fernandes Bioinformatics Training Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL http://gtpb.igc.gulbenkian.pt

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ELIXIR-EXCELLERAE TtT, August 20-21, Antwerp
by Mateusz Kuzak 09 Jul '18

09 Jul '18

Dear all, I’m pleased to announce the Train the Trainer (TtT) event organised by ELIXIR-EXCELERATE, ELIXIR-Belgium and ELIXIR-NL. Date: August 20-21, 2018 Venue: Antwerp, Belgium Full details and the application form at: https://www.eventbrite.com/e/elixir-excelerate-train-the-trainer-registrati… The course will be taught by Paula Martinez from VIB and ELIXIR-Belgium and myself. This workshop is a great way to improve teaching skills and learn modern, evidence based pedagogy. Should be of interest for anyone who teaches at various training, gives lectures or designs learning content. COURSE DESCRIPTION: The course is organized around four sessions, covering: * Learning principles and how they apply to training and teaching * Teaching techniques that can be used to enhance learner engagement and participation * Assessment and feedback in training and teaching * Lesson, course, and materials design Examples and discussions will also focus on the challenges presented by academic teaching. Who may be interested in this course? Whoever wants to become a teacher or a better one. If you have questions like the following ones, this course may be very helpful to you. * How learning works? * How can I use learning principles to improve my teaching? * How can I make my teaching more engaging and effective? * How should I adjust my teaching to different types of learners? * How can I help slow learners? * How can I assess whether my students are actually understanding my lessons? Are they actually learning? * What is the best balance between theory and practice? * How can I best assess whether learning is occurring and/or has occurred? * What works in a classroom and what doesn’t? * Etc. This course is meant to offer guidance, ideas and tips for training/teaching design, development and delivery based on research-driven educational principles. There is no course attendance fee. The participants will need to bear their travel, hotel (if any) and meal costs. Candidates from ELIXIR nodes might apply for an ELIXIR Staff Exchange Programme Travel Grant when they fill their application form. Apologise for cross-posting. Mateusz — Mateusz Kuzak Scientific Community Manager | Dutch Techcentre for Life Sciences e-mail: mateusz.kuzak(a)dtls.nl | tel. +31 643707254 twitter: @matkuzak | github: mkuzak | skype: mkuzak Visting address: DTL | Jaarbeurs Innovation Mile (JIM) | 6th floor Beatrixgebouw Jaarbeursplein 6 | 3521 AL Utrecht

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Fwd: postdoc opportunity
by Patrick Deelen 06 Jul '18

06 Jul '18

---------- Forwarded message ---------- From: Gosia Trynka <gosia(a)sanger.ac.uk> Date: Fri, Jul 6, 2018 at 12:34 PM Subject: postdoc opportunity To: "patrickdeelen(a)gmail.com" <patrickdeelen(a)gmail.com> Zam Iqbal at EBI and myself at Sanger Institute, are recruiting for an ESPOD position. These are prestigious fellowships that give a unique opportunity to work closely with groups at the two Institutes which are located at the Wellcome Genome Campus. We are recruiting for a postdoc to lead on a very exciting project, assessing gene regulation in the MHC region using variation graphs. Zam is one of the leaders in the field of variation graphs algorithms. Whilst my group has strong expertise in gene expression regulation in the context of immune cells and linking these effects with immune disease variants. This is an opportunity to apply algorithms at the forefront of sequence alignment methods to a wide variety of functional genomics data generated in my group and deposited in public resources, to ultimately help interpret the function of immune-disease associated variants. More details about the project can be found in this link: https://www.embl.de/jobs/pdf/ESPOD_Fellowship_project_4.pdf Get in touch if you have any questions. Please apply if this sounds exciting, the deadline is approaching soon, July 20th. Best regards, Gosia

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interested in shaping your trainers' capacities - announcement of train the trainer events this year
by Alexander Botzki 04 Jul '18

04 Jul '18

Hi all, on behalf of colleagues from ELIXIR training, please see below the announcements. Cheers, Alex COURSE ANNOUNCEMENT ELIXIR-EXCELERATE is pleased to announce the following Train the Trainer (TtT) events: - August 20-21, 2018 Venue: Antwerp, Belgium Full details and the application form at: https://www.eventbrite.com/e/elixir-excelerate-train-the-trainer-registrati… - September 27-28, 2018 Venue: Italian National Research Council (CNR), Rome, Italy Full details and the application form at: https://elixir-iib-training.github.io/website/2018/09/27/train-the-trainer-… - October 9-11, 2018 (2 days) Venue: Science for Life Laboratory, Solna, Sweden Full details and the application form at: https://elixir-iib-training.github.io/website/2018/10/09/train-the-trainer-… COURSE DESCRIPTION: The course is organized around four sessions, covering: * Learning principles and how they apply to training and teaching * Teaching techniques that can be used to enhance learner engagement and participation * Assessment and feedback in training and teaching * Lesson, course, and materials design Examples and discussions will also focus on the challenges presented by academic teaching. Who may be interested in this course? Whoever wants to become a teacher or a better one. If you have questions like the following ones, this course may be very helpful to you. * How learning works? * How can I use learning principles to improve my teaching? * How can I make my teaching more engaging and effective? * How should I adjust my teaching to different types of learners? * How can I help slow learners? * How can I assess whether my students are actually understanding my lessons? Are they actually learning? * What is the best balance between theory and practice? * How can I best assess whether learning is occurring and/or has occurred? * What works in a classroom and what doesn't? * Etc. This course is meant to offer guidance, ideas and tips for training/teaching design, development and delivery based on research-driven educational principles. There is no course attendance fee. The participants will need to bear their travel, hotel (if any) and meal costs. Candidates from ELIXIR nodes might apply for an ELIXIR Staff Exchange Programme Travel Grant<https://docs.google.com/document/d/1YbbHoH2YYbM6sbPGypOTkIcNToYXo5XPcn99CSV…> when they fill their application form. We apologise for cross-posting. Thank you for your interest, kind regards, Loredana Le Pera. (ELIXIR-IIB Training Coordinator Deputy)

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bioinfo/biostatistician job at the University of Luxembourg
by Aurélien GINOLHAC 02 Jul '18

02 Jul '18

Dear all, The Life Sciences Research Unit of the University of Luxembourg is looking for a bioinfo/biostatistician. Fixed term contract of 3 + 2 years. Enthusiasm and knowledge of R required. All details here: http://emea3.mrted.ly/1vsqq <https://t.co/oSTeBBA0Tn> Best regards, Aurelien Ginolhac -- University of Luxembourg Faculty of Science, Technology and Communication Life Science Research Unit Campus Belval, Biotech II – Office 4.22 6, Avenue du Swing L-4367 Belvaux Phone: (+352) 46 66 44 6560

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